What you describe sounds like a database of information.
The organization/navigation of the site may be totally different than the organization of the content especially where there is a database of information/content. So, you may need to think about how viewers will use your website (from the user`s point of view).
The structure of your content...what folders etc. is important so you can find information, but it may not be realted to the navigation of the website.
Content may be pulled based upon search criteria... where the site`s navigation for that may simply be a link to a search page.